Method for calculating the effect of a rigid enzyme on the dynamics of a large DNA helix

The Green-function technique is used to study the interbase H-bond stretch of poly(dA)-poly(dT) and poly(dT-dA)-poly(dT-dA) when an effective enzyme is attached to the helices, where A is adenine and T is thymine. Three different two-atom attachment points are studied. The response is an enhanced interbase H-bond stretch amplitude when the effective enzyme is attached to the helix in poly(dT-dA)-poly(dT-dA). Then a 28-atom attachment to the helix is studied. This corresponds to an enzyme in contact with a 70-base-pair stretch of the helix. A large response is again found for the alternating polymer. This may relate to the fact that biological promoter sites often contain alternating TA sequences. The interbase H-bond stretch is studied as this motion is closely related to the helix transition to the open state involved in a number of biological processes.